From 2e2dcd546b2aa297b8d054a6fd44def0f07efb70 Mon Sep 17 00:00:00 2001
From: jgugliel <julien.guglielmini@pasteur.fr>
Date: Fri, 17 Jun 2022 10:24:36 +0200
Subject: [PATCH] README update
---
README.md | 9 +++++----
1 file changed, 5 insertions(+), 4 deletions(-)
diff --git a/README.md b/README.md
index fdfd2c8..4f1d5a1 100644
--- a/README.md
+++ b/README.md
@@ -7,11 +7,12 @@ wGRR is a set of scripts to calculate the weighted Gene Repertoire Relatedness (
wGRR(A,B) = \frac{\sum_{i}{id(A_i,B_i)}}{min(P_A,P_B)}
```
where
-* $`id(A_i,B_i)`$ is the identity score for each BBH pair between element $`A`$ and element $`B`$
-* $`min(P_A,P_B)`$ is the number of proteins in the smallest of $`A`$ and $`B`$ elements.
+* $`i`$ is the number of BBH between elements $`A`$ and $`B`$
+* $`id(A_i,B_i)`$ is the identity score of BBH $`i`$
+* $`P_A`$ and $`P_B`$ are the numbers of proteins of $`A`$ and $`B`$ respectively
**NOTE**
-`wGRR` calculates 3 versions of the wGRR depending on which BBH pairs are considered (numerator) and what proteins should be counted (denominator). See the `Output` section of this manual for more explanations.
+`wGRR` calculates 3 versions of the wGRR score depending on which BBH are considered (numerator) and what proteins should be counted (denominator). See the `Output` section of this manual for more explanations.
### Dependencies
BBH are defined by all versus all protein comparisons using [MMseqs2][1].
@@ -105,6 +106,6 @@ wGRR3 also uses the protein families. But this time, if two BBH pairs are found
Common3 is the number of protein families containing at least one BBH divided by the mean nProt3 of two elements.
-
+
[1]: https://mmseqs.com/
--
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